Structural, functional, phylogenetic, and molecular dynamic simulation study of PEST-containing nuclear protein: An e-science view

PEST-containing nuclear protein (PCNP) is a short-lived novel nuclear protein. It has been well evaluated that PCNP mediates the progression of several cancers, but the exact mechanisms are still under investigation. In this study, we provided an e-science view of PCNP protein from the aspects of protein structure, interactions, and bioinformatics-based analysis related to evolutionary features as well as proteomic profile. The phylogenetic relationship results reveal that PCNP is closely related to Pan troglodytes and the Bovidae family, while being distantly related to the Muridae family. The analysis of the physicochemical properties of PCNP demonstrated that it is a thermolabile protein which is slightly acidic and hydrophilic in nature. Further, coexpression and protein-protein interaction analyses were carried out, which demonstrated that the PCNP gene was remarkably expressed with MORF4LI and RSL24D1 genes and has close interactions with TRAM1, PSMC6, SRP9, PRKRIR, UHRF2, and BMI1 proteins. Gene ontology and pathway enrichment analyses showed that PCNP has a high tendency to work in cell cycle regulation. Moreover, among the four 3D structure generating tools, I-TASSER-generated structure had the highest quality factor score. The validation analysis revealed that the I-TASSER-generated structure exhibited the best quality factor score with maximum amino acids in the favored region. In addition, molecular dynamic simulation analysis approved the stable structure of the PCNP. This is the first study that highlights the usefulness of the understanding of the structural and functional analysis of the PCNP, which lays the groundwork for further experimental studies to validate the outcome.